At least three people were killed and dozens seriously injured after the boat blew up near Ashmore Reef, about 800km west of Darwin, on Thursday morning. At least two people are missing.

The boat was carrying 47 asylum seekers - mostly men believed to be from Afghanistan - and two crew. It had been intercepted by the Australian navy and was being escorted to the country's detention centre at Christmas Island in the Indian Ocean.

By Friday afternoon, most of the 44 known injured were in hospitals in Darwin, Perth, Broome and Brisbane. Many are suffering from severe burns and some are on life support.

Up to four Royal Australian Navy personnel have less severe injuries.

West Australian Premier Colin Barnett said it was believed the wooden boat was doused with petrol by those on board before the explosion occurred.

However, Immigration Minister Chris Evans told the ABC it was too early to speculate and the cause is not going to be known for some time.

Navy and police are investigating the incident.

Australian Prime Minister Kevin Rudd condemned people smugglers, describing those who take money from those seeking asylum as the "absolute scum of the earth".

The boat is the sixth arrival of suspected asylum seekers in Australian waters this year.

Meanwhile, 68 Afghans have been arrested near Jakarta as they prepared to travel to Australia, the Indonesian authorities say. Indonesia has long been a transit country for illegal migration and people smuggling to Australia.